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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $species_info = array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ) $local_species = 'shi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $species_info = array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ) $local_species = 'shi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ), 'gf_id' => 'HOM05D001196', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001196' ), 'data_identifier' => 'HOM05D001196', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001196', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18240' => 'bna', 'A02p10040' => 'bna', 'A03p14420' => 'bna', 'A04p32740' => 'bna', 'A05p03800' => 'bna', 'A05p28090' => 'bna', 'A07p00290' => 'bna', 'A07p12120' => 'bna', 'A09p12900' => 'bna', 'A09p51840' => 'bna', 'Aa31LG10G13890' => 'aar', 'Aa31LG1G25230' => 'aar', 'Aa31LG2G21840' => 'aar', 'Aa31LG3G10710' => 'aar', 'Aa31LG5G10310' => 'aar', 'Aa31LG8G17410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3760' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.534' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3875' => 'aag', 'Actinidia07313' => 'ach', 'Actinidia09925' => 'ach', 'Actinidia10716' => 'ach', 'Actinidia26499' => 'ach', 'Actinidia34576' => 'ach', 'Actinidia37525' => 'ach', 'Actinidia37526' => 'ach', 'Ah.08g213530' => 'amhyb', 'AL3G53420' => 'aly', 'AL4G42240' => 'aly', 'AL5G41500' => 'aly', 'AL7G24000' => 'aly', 'AL7G25700' => 'aly', 'AL8G30210' => 'aly', 'Aqoxy2G01847' => 'aox', 'Aqoxy2G03695' => 'aox', 'Aqoxy428s001' => 'aox', 'Aqoxy4G01974' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0RK6BN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G2X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DI4MXM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KT0MEF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR1R6N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N57GQA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUM03Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1GN2M' => 'arhy', 'AT2G20440' => 'ath', 'AT2G43490' => 'ath', 'AT3G59570' => 'ath', 'AT4G27100' => 'ath', 'AT4G28550' => 'ath', 'AT5G54780' => 'ath', 'ATR0697G130' => 'atr', 'ATR0736G219' => 'atr', 'ATR0743G212' => 'atr', 'Atru.chr2.3234' => 'acertr', 'Atru.chr4.1298' => 'acertr', 'Atru.chr4.1299' => 'acertr', 'Atru.chr5.1756' => 'acertr', 'AUR62002362' => 'cqu', 'AUR62008751' => 'cqu', 'AUR62015670' => 'cqu', 'AUR62020533' => 'cqu', 'AUR62023823' => 'cqu', 'AUR62025487' => 'cqu', 'BcaB01g04324' => 'bca', 'BcaB02g08936' => 'bca', 'BcaB03g12580' => 'bca', 'BcaB03g16840' => 'bca', 'BcaB05g22157' => 'bca', 'BcaB06g29316' => 'bca', 'BcaB06g29318' => 'bca', 'BcaB07g31585' => 'bca', 'BcaB08g35840' => 'bca', 'BcaB08g35843' => 'bca', 'BcaC01g06326' => 'bca', 'BcaC02g07175' => 'bca', 'BcaC02g12388' => 'bca', 'BcaC03g14289' => 'bca', 'BcaC03g17588' => 'bca', 'BcaC04g19369' => 'bca', 'BcaC04g22787' => 'bca', 'BcaC05g28292' => 'bca', 'BcaC06g36734' => 'bca', 'BcaC07g38340' => 'bca', 'BcaC07g38341' => 'bca', 'BcaC07g38342' => 'bca', 'BcaC07g40467' => 'bca', 'BcaC07g40482' => 'bca', 'BcaC07g40484' => 'bca', 'BcaC09g50617' => 'bca', 'BcaNung03060' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01100' => 'bna', 'BolC1t02257H' => 'bol', 'BolC2t07775H' => 'bol', 'BolC3t14099H' => 'bol', 'BolC4t22083H' => 'bol', 'BolC4t28549H' => 'bol', 'BolC5t31904H' => 'bol', 'BolC5t33072H' => 'bol', 'BolC7t40503H' => 'bol', 'BolC8t51058H' => 'bol', 'BolC9t54437H' => 'bol', 'BolC9t57394H' => 'bol', 'BraA01t01779Z' => 'bra', 'BraA02t06073Z' => 'bra', 'BraA03t10738Z' => 'bra', 'BraA04t18738Z' => 'bra', 'BraA05t19368Z' => 'bra', 'BraA05t21691Z' => 'bra', 'BraA08t33958Z' => 'bra', 'BraA09t36935Z' => 'bra', 'BraA09t40619Z' => 'bra', 'C01p23240' => 'bna', 'C02p16690' => 'bna', 'C03p16790' => 'bna', 'C04p04500' => 'bna', 'C04p70450' => 'bna', 'C05p31780' => 'bna', 'C05p43490' => 'bna', 'C08p10940' => 'bna', 'C08p34560' => 'bna', 'C09p15290' => 'bna', 'C09p45190' => 'bna', 'C09p56460' => 'bna', 'CAN.G1070.2' => 'can', 'CAN.G1070.3' => 'can', 'CAN.G1781.15' => 'can', 'CAN.G2112.1' => 'can', 'CAN.G316.11' => 'can', 'CAN.G316.12' => 'can', 'CAN.G337.97' => 'can', 'CAN.G941.8' => 'can', 'CANSAT20G0001' => 'cansat', 'CANSAT35G0672' => 'cansat', 'CANSAT78G2205' => 'cansat', 'CARHR110990' => 'chi', 'CARHR138580' => 'chi', 'CARHR169960' => 'chi', 'CARHR234750' => 'chi', 'CARHR236330' => 'chi', 'CARHR268110' => 'chi', 'Carub.0003s3483' => 'cru', 'Carub.0004s2595' => 'cru', 'Carub.0007s1213' => 'cru', 'Carub.0007s1374' => 'cru', 'Carub.0008s1505' => 'cru', 'Ca_01241_v3' => 'car', 'Ca_01738_v3' => 'car', 'Ca_09664_v3' => 'car', 'Ca_18856_v3' => 'car', 'CBR_g16128' => 'cbr', 'Cc01_g18100' => 'ccan', 'Cc03_g12480' => 'ccan', 'Cc05_g13350' => 'ccan', 'CDE02G4724' => 'cde', 'CDE03G0259' => 'cde', 'CDE04G3510' => 'cde', 'CDE04G3701' => 'cde', 'CDE05G1690' => 'cde', 'CDE05G3539' => 'cde', 'CDE09G1175' => 'cde', 'Cfa015208' => 'cfa', 'Ciclev10008337m.g' => 'ccl', 'Ciclev10018989m.g' => 'ccl', 'Ciclev10020291m.g' => 'ccl', 'CiPaw.01G095000' => 'cil', 'CiPaw.03G267200' => 'cil', 'CiPaw.11G185100' => 'cil', 'CiPaw.12G127200' => 'cil', 'ClCG09G008460' => 'cla', 'ClCG10G005620' => 'cla', 'COL.COLO4_04013' => 'col', 'COL.COLO4_06574' => 'col', 'COL.COLO4_09589' => 'col', 'Cpa.g.sc1040.2' => 'cpa', 'Cpa.g.sc165.28' => 'cpa', 'Cpa.g.sc97.51' => 'cpa', 'CsaV3_3G005320' => 'csa', 'CsaV3_4G002540' => 'csa', 'CsaV3_7G026600' => 'csa', 'CSS0000247' => 'camsi', 'CSS0010815' => 'camsi', 'CSS0015237' => 'camsi', 'CSS0026555' => 'camsi', 'CSS0038168' => 'camsi', 'CSS0044723' => 'camsi', 'DCAR_000922' => 'dca', 'DCAR_000923' => 'dca', 'DCAR_005680' => 'dca', 'DCAR_022533' => 'dca', 'DCAR_029914' => 'dca', 'Dinv05090' => 'din', 'Dinv22293' => 'din', 'Dinv34647' => 'din', 'Dinv40724' => 'din', 'Dinv44162' => 'din', 'Duzib138G0438' => 'dzi', 'Duzib151G0336' => 'dzi', 'Duzib170G0868' => 'dzi', 'Duzib213G0104' => 'dzi', 'Duzib268G0677' => 'dzi', 'ECA236G1590' => 'eca', 'ECA240G1795' => 'eca', 'ECA240G2714' => 'eca', 'ECA248G2488' => 'eca', 'EL10Ac3g06026' => 'bvu', 'EL10Ac4g07938' => 'bvu', 'EL10Ac7g17621' => 'bvu', 'Eucgr.B01568' => 'egr', 'Eucgr.F00973' => 'egr', 'Eucgr.F03436' => 'egr', 'Eucgr.H00337' => 'egr', 'FAN11G3046' => 'fan', 'FAN15G1078' => 'fan', 'FAN16G2460' => 'fan', 'FAN20G0996' => 'fan', 'FAN21G0397' => 'fan', 'FAN24G0599' => 'fan', 'FAN24G1294' => 'fan', 'FAN24G3245' => 'fan', 'FAN25G2728' => 'fan', 'FAN27G3267' => 'fan', 'FvH4_2g21100' => 'fve', 'FvH4_3g21970' => 'fve', 'Glyma.06G269900' => 'gma', 'Glyma.10G038700' => 'gma', 'Glyma.12G134900' => 'gma', 'Glyma.12G213300' => 'gma', 'Glyma.13G125100' => 'gma', 'Glyma.13G288400' => 'gma', 'Glyma.13G346200' => 'gma', 'Glyma.15G028000' => 'gma', 'Gohir.A01G075900' => 'ghi', 'Gohir.A02G092901' => 'ghi', 'Gohir.A04G020900' => 'ghi', 'Gohir.A07G214200' => 'ghi', 'Gohir.A08G020000' => 'ghi', 'Gohir.A10G141100' => 'ghi', 'Gohir.A11G131950' => 'ghi', 'Gohir.A11G279100' => 'ghi', 'Gohir.D01G063200' => 'ghi', 'Gohir.D02G111200' => 'ghi', 'Gohir.D05G365800' => 'ghi', 'Gohir.D07G220700' => 'ghi', 'Gohir.D08G030600' => 'ghi', 'Gohir.D10G125800' => 'ghi', 'Gohir.D11G137833' => 'ghi', 'Gohir.D11G137900' => 'ghi', 'Gohir.D11G290000' => 'ghi', 'Gorai.001G255000' => 'gra', 'Gorai.002G083900' => 'gra', 'Gorai.004G028200' => 'gra', 'Gorai.005G126100' => 'gra', 'Gorai.007G148000' => 'gra', 'Gorai.007G313900' => 'gra', 'Gorai.009G426300' => 'gra', 'Gorai.011G138800' => 'gra', 'GSVIVG01001980001' => 'vvi', 'GSVIVG01002818001' => 'vvi', 'GSVIVG01004096001' => 'vvi', 'GSVIVG01004111001' => 'vvi', 'GSVIVG01028367001' => 'vvi', 'HanXRQChr03g0077321' => 'han', 'HanXRQChr03g0089131' => 'han', 'HanXRQChr10g0305301' => 'han', 'HanXRQChr11g0337891' => 'han', 'HanXRQChr13g0407681' => 'han', 'Haze_01426' => 'cav', 'Haze_01427' => 'cav', 'Haze_01428' => 'cav', 'Haze_01430' => 'cav', 'Haze_01431' => 'cav', 'Haze_09631' => 'cav', 'Haze_09632' => 'cav', 'Haze_24659' => 'cav', 'Haze_24660' => 'cav', 'Hma1.2p1_0487F.1_g163530' => 'hma', 'Hma1.2p1_1344F.1_g277080' => 'hma', 'HPP92_001784' => 'vpl', 'HPP92_004649' => 'vpl', 'HPP92_010100' => 'vpl', 'HPP92_025748' => 'vpl', 'Hund02120' => 'sun', 'Hund03184' => 'sun', 'Hund05463' => 'sun', 'Hund12380' => 'sun', 'Hund23296' => 'sun', 'Lalb_Chr01g0006091' => 'lal', 'Lalb_Chr03g0030091' => 'lal', 'Lalb_Chr03g0030101' => 'lal', 'Lalb_Chr06g0170581' => 'lal', 'Lalb_Chr14g0366211' => 'lal', 'Lalb_Chr14g0372601' => 'lal', 'Lalb_Chr21g0313981' => 'lal', 'Lalb_Chr24g0396661' => 'lal', 'Lalb_Chr24g0396671' => 'lal', 'Lj1C867T7' => 'lonja', 'Lj2A1147T78' => 'lonja', 'Lj2g0002617' => 'lja', 'Lj3A109T10' => 'lonja', 'Lj3A116G12' => 'lonja', 'Lj3C109T1' => 'lonja', 'Lj3C116T2' => 'lonja', 'Lj3g0006119' => 'lja', 'Lj3g0007348' => 'lja', 'Lj3g0018788' => 'lja', 'Lj5g0020927' => 'lja', 'Lj8A166T92' => 'lonja', 'Lsat_1_v5_gn_0_6780' => 'lsa', 'Lsat_1_v5_gn_3_111301' => 'lsa', 'Lsat_1_v5_gn_4_185761' => 'lsa', 'Lsat_1_v5_gn_4_185780' => 'lsa', 'Lsat_1_v5_gn_5_182761' => 'lsa', 'Lsat_1_v5_gn_7_108921' => 'lsa', 'Manes.03G123918' => 'mes', 'Manes.04G048209' => 'mes', 'Manes.11G126700' => 'mes', 'Manes.12G034300' => 'mes', 'Manes.13G036300' => 'mes', 'Manes.15G075400' => 'mes', 'Mapoly0056s0046' => 'mpo', 'Mapoly0202s0005' => 'mpo', 'Mapoly0202s0008' => 'mpo', 'MBI02_g23960_MAGBIO' => 'mbi', 'MBI07_g05956_MAGBIO' => 'mbi', 'MBI07_g05958_MAGBIO' => 'mbi', 'MBI07_g31091_MAGBIO' => 'mbi', 'MCO16G493' => 'mco', 'MD03G1209800' => 'mdo', 'MD04G1046500' => 'mdo', 'MD05G1194200' => 'mdo', 'MD10G1180900' => 'mdo', 'MD11G1224500' => 'mdo', 'MD13G1269900' => 'mdo', 'Medtr1g069705' => 'mtr', 'Medtr1g072400' => 'mtr', 'Medtr2g083220' => 'mtr', 'Medtr2g099185' => 'mtr', 'Medtr4g079330' => 'mtr', 'Medtr4g081110' => 'mtr', 'MELO3C017792.2' => 'cme', 'MELO3C019228.2' => 'cme', 'MELO3C021110.2' => 'cme', 'MELO3C025077.2' => 'cme', 'MELO3C025406.2' => 'cme', 'Migut.D00448' => 'egut', 'Migut.G01291' => 'egut', 'Migut.H01849' => 'egut', 'Migut.M01797' => 'egut', 'MSTRG.14422' => 'ama', 'MSTRG.18334' => 'ama', 'MSTRG.6896' => 'ama', 'MSTRG.9746' => 'ama', 'Nitab4.5_0000092g0050' => 'nta', 'Nitab4.5_0000115g0020' => 'nta', 'Nitab4.5_0000326g0200' => 'nta', 'Nitab4.5_0000397g0250' => 'nta', 'Nitab4.5_0001479g0080' => 'nta', 'Nitab4.5_0001945g0010' => 'nta', 'Nitab4.5_0002229g0230' => 'nta', 'Nitab4.5_0002342g0050' => 'nta', 'Nitab4.5_0003016g0010' => 'nta', 'Nitab4.5_0006380g0010' => 'nta', 'Nitab4.5_0006655g0040' => 'nta', 'Nitab4.5_0012021g0010' => 'nta', 'Nn1g02885' => 'nnu', 'Nn1g03608' => 'nnu', 'Nn1g07060' => 'nnu', 'Nn1g09532' => 'nnu', 'Nn1g09558' => 'nnu', 'Nn3g19706' => 'nnu', 'Nn7g37564' => 'nnu', 'Oeu007635.2' => 'oeu', 'Oeu015640.1' => 'oeu', 'Oeu015641.1' => 'oeu', 'Oeu020783.1' => 'oeu', 'Oeu032445.1' => 'oeu', 'Oeu034455.1' => 'oeu', 'Oeu035733.1' => 'oeu', 'Oeu045247.1' => 'oeu', 'Os01g0100100' => 'osa', 'Os02g0810500' => 'osa', 'Os07g0525400' => 'osa', 'Os11g0587500' => 'osa', 'Peaxi162Scf00058g01216' => 'pax', 'Peaxi162Scf00058g01217' => 'pax', 'Peaxi162Scf00407g00017' => 'pax', 'Peaxi162Scf00407g00211' => 'pax', 'Peaxi162Scf00415g00011' => 'pax', 'Peaxi162Scf00450g00866' => 'pax', 'Peaxi162Scf03993g00008' => 'pax', 'PGR031G0615' => 'pgr', 'PGR031G3955' => 'pgr', 'PGR083G1705' => 'pgr', 'PGSC0003DMG400001042' => 'stu', 'PGSC0003DMG400014398' => 'stu', 'PGSC0003DMG400025622' => 'stu', 'PGSC0003DMG401010311' => 'stu', 'PGSC0003DMG402010311' => 'stu', 'PGSC0003DMG402014716' => 'stu', 'Phvul.005G092600' => 'pvu', 'Phvul.005G155000' => 'pvu', 'Phvul.007G191100' => 'pvu', 'Phvul.011G139200' => 'pvu', 'Potri.001G419100' => 'ptr', 'Potri.005G227400' => 'ptr', 'Potri.007G132900' => 'ptr', 'Potri.011G135300' => 'ptr', 'Potri.017G023200' => 'ptr', 'Pp3c13_11070' => 'ppa', 'Pp3c1_2510' => 'ppa', 'Pp3c26_10860' => 'ppa', 'Pp3c3_9290' => 'ppa', 'Prupe.1G200000' => 'ppe', 'Prupe.4G205400' => 'ppe', 'Prupe.8G220800' => 'ppe', 'Psat5g252080' => 'psa', 'Psat5g290800' => 'psa', 'Psat6g062320' => 'psa', 'Psat7g162640' => 'psa', 'PSO017G4430' => 'pso', 'PSO017G4546' => 'pso', 'PSO063G5743' => 'pso', 'PSO210G1308' => 'pso', 'PSO832G1595' => 'pso', 'PSO837G0034' => 'pso', 'QL08p012720' => 'qlo', 'QL08p012860' => 'qlo', 'QL09p040085' => 'qlo', 'QL10p051768' => 'qlo', 'RcHm_v2.0_Chr5g0037821' => 'rch', 'RcHm_v2.0_Chr6g0287601' => 'rch', 'Rhsim02G0082700' => 'rsi', 'Rhsim13G0036900' => 'rsi', 'RhsimUnG0252500' => 'rsi', 'Sabra05G0175500' => 'sbr', 'Sabra07G0107900' => 'sbr', 'Sabra07G0119700' => 'sbr', 'Sabra11G0121100' => 'sbr', 'Sabra16G0284600' => 'sbr', 'SalBow1G4244' => 'sbo', 'SalBow2G0725' => 'sbo', 'SalBow2G3091' => 'sbo', 'SalBow5G3114' => 'sbo', 'SalBow5G3203' => 'sbo', 'Sc03g0008870' => 'sci', 'Sc05g0003230' => 'sci', 'Sc07g0002750' => 'sci', 'Sc13g0007940' => 'sci', 'Sed0014037' => 'sed', 'Sed0015782' => 'sed', 'Sed0017758' => 'sed', 'Sed0022994' => 'sed', 'SEGI_17446' => 'sgi', 'SEGI_38230' => 'sgi', 'SGA_v2.0_scaffold138G35206' => 'sas', 'SGA_v2.0_scaffold283G46997' => 'sas', 'SGA_v2.0_scaffold696G53472' => 'sas', 'SGA_v2.0_scaffold9G05045' => 'sas', 'SHI09740' => 'shi', 'SHI31833' => 'shi', 'SMO146G0333' => 'smo', 'Solyc03g058470.3' => 'sly', 'Solyc03g058500.1' => 'sly', 'Solyc06g008250.3' => 'sly', 'Solyc07g064230.4' => 'sly', 'Solyc09g066420.3' => 'sly', 'Solyc10g006440.3' => 'sly', 'Solyc12g005220.2' => 'sly', 'Sopen03g012120' => 'spe', 'Sopen06g003110' => 'spe', 'Sopen07g032380' => 'spe', 'Sopen09g028140' => 'spe', 'Sopen10g002390' => 'spe', 'Sopen12g001200' => 'spe', 'Sp3g33660' => 'spa', 'Sp4g25580' => 'spa', 'Sp5g03580' => 'spa', 'Sp6g16720' => 'spa', 'Sp7g25070' => 'spa', 'Sp7g26530' => 'spa', 'TAR362G0635' => 'tar', 'TAR624G0789' => 'tar', 'TAR626G1812' => 'tar', 'TAR633G0459' => 'tar', 'TAR633G0590' => 'tar', 'THA.LOC104802319' => 'tha', 'THA.LOC104804043' => 'tha', 'THA.LOC104805352' => 'tha', 'THA.LOC104812528' => 'tha', 'THA.LOC104817651' => 'tha', 'Thecc.01G254600' => 'tca', 'Thecc.04G172200' => 'tca', 'Thecc.07G050400' => 'tca', 'Thhalv10001327m.g' => 'esa', 'Thhalv10001992m.g' => 'esa', 'Thhalv10013605m.g' => 'esa', 'Thhalv10025248m.g' => 'esa', 'Thhalv10025292m.g' => 'esa', 'TPR.G19969' => 'tpr', 'TPR.G24741' => 'tpr', 'TPR.G35712' => 'tpr', 'TPR.G6502' => 'tpr', 'TWI15G0546' => 'twi', 'TWI38G2411' => 'twi', 'TWI39G1309' => 'twi', 'TWI75G0865' => 'twi', 'unitig_26.g9965' => 'ugi', 'unitig_52.g17673' => 'ugi', 'unitig_749.g13731' => 'ugi', 'vmacro02681' => 'vma', 'vmacro09742' => 'vma', 'vmacro11758' => 'vma', 'VMungo0720G3159' => 'vmu', 'VMungo1080G0337' => 'vmu', 'VMungo1080G0844' => 'vmu', 'VMungo1127G0550' => 'vmu', 'VMungo1127G2285' => 'vmu', 'Zm00001eb065390' => 'zma', 'Zm00001eb106230' => 'zma', 'Zm00001eb127200' => 'zma', 'Zm00001eb258440' => 'zma', 'Zm00001eb323030' => 'zma' ) $gf_id = 'HOM05D001196' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001196' ) $data_identifier = 'HOM05D001196' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 23, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 11, 'bra' => (int) 9, 'can' => (int) 8, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 9, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 9, 'lonja' => (int) 7, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 12, 'nnu' => (int) 7, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323030' $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